Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2227
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 151494
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
File 2 of 2
Found at i:131047 original size:27 final size:27
Alignment explanation
Indices: 131003--131103 Score: 98
Period size: 27 Copynumber: 3.7 Consensus size: 27
130993 TAATAATGAA
*
131003 AAATCAAAAAATTAAAAAAAAAATCAAT
1 AAATCAAAAAAAT-AAAAAAAAATCAAT
* *
131031 GAATCAAAAAAATAAAAAAAAATCATT
1 AAATCAAAAAAATAAAAAAAAATCAAT
* * * *
131058 AAATCAAAGATATAAAATCAAAAT-AAA
1 AAATCAAAAAAATAAAA-AAAAATCAAT
*
131085 AAAT-AATAAAATAAAAAAA
1 AAATCAAAAAAATAAAAAAA
131104 TGATGATAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
25 2 0.03
26 9 0.15
27 32 0.54
28 16 0.27
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (27 bp):
AAATCAAAAAAATAAAAAAAAATCAAT
Found at i:131641 original size:35 final size:35
Alignment explanation
Indices: 131602--131671 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
131592 AAAATGAGGC
* *
131602 AGCATCGAAGAGCAGCAAGGAGCTGCAAAGCAACA
1 AGCATCGAAGAACAGCAAGGAGCTGCAAAGAAACA
*** *
131637 AGCATCGGTTAACAGCATGGAGCTGCAAAGAAACA
1 AGCATCGAAGAACAGCAAGGAGCTGCAAAGAAACA
131672 GGAAAACAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.27, T:0.10
Consensus pattern (35 bp):
AGCATCGAAGAACAGCAAGGAGCTGCAAAGAAACA
Found at i:131762 original size:57 final size:57
Alignment explanation
Indices: 131693--131809 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
131683 AAAAAGGAAG
131693 ATGAACAGCAACTCCAGCAATAGCAGCAACACCGAATTCACAACAGTTTCAGCAAGC
1 ATGAACAGCAACTCCAGCAATAGCAGCAACACCGAATTCACAACAGTTTCAGCAAGC
131750 ATGAACAGCAACTCCAGCAATAGCAGCAACACCGAATTCACAACAGTTTCAGCAAGC
1 ATGAACAGCAACTCCAGCAATAGCAGCAACACCGAATTCACAACAGTTTCAGCAAGC
131807 ATG
1 ATG
131810 CAACCAATAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.40, C:0.29, G:0.16, T:0.15
Consensus pattern (57 bp):
ATGAACAGCAACTCCAGCAATAGCAGCAACACCGAATTCACAACAGTTTCAGCAAGC
Found at i:133410 original size:97 final size:96
Alignment explanation
Indices: 133267--133529 Score: 366
Period size: 97 Copynumber: 2.7 Consensus size: 96
133257 CGATGATACA
* **
133267 CTAACCCCATTCTTCTAAGGGGATACTCCAACCCTGTTTTTAAACTTATTC-AAATTTAAATCTT
1 CTAA-CCCATTCTTCTGAGGGGATACTCCAACCCCATTTTTAAACTTA-TCAAAATTTAAATCTT
* *
133331 ATTTTCGGTTAAATTGTCATCATCGGGGACGCT
64 ATTTTCGGTTAAATTGTCATCATCGGGAACACT
* *
133364 CTAATCCCATTCCTCTGAGGGGATACTCCAACCCCATTTTTAAACTTATCAAAATTTAAATTTTA
1 CTAA-CCCATTCTTCTGAGGGGATACTCCAACCCCATTTTTAAACTTATCAAAATTTAAATCTTA
*
133429 TTTTCGGTTAAATTGTCATCATCGTGAACACT
65 TTTTCGGTTAAATTGTCATCATCGGGAACACT
* * * * *
133461 CCAACCCTATTCTTTTGAGGGGATACTCCAACCCCATTTTTAAAGTCATCAAAATTTAAATCTTC
1 CTAACCC-ATTCTTCTGAGGGGATACTCCAACCCCATTTTTAAACTTATCAAAATTTAAATCTTA
133526 TTTT
65 TTTT
133530 GTCCAAATTA
Statistics
Matches: 148, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
96 5 0.03
97 143 0.97
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (96 bp):
CTAACCCATTCTTCTGAGGGGATACTCCAACCCCATTTTTAAACTTATCAAAATTTAAATCTTAT
TTTCGGTTAAATTGTCATCATCGGGAACACT
Found at i:133626 original size:69 final size:69
Alignment explanation
Indices: 133482--133617 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 69
133472 CTTTTGAGGG
* *
133482 GATACTCCAACCCCATTTTTAAAGTCATCAAAATTTAAATCTTCTTTTGTCCAAATTATCATTGT
1 GATACTCCAACCCCATTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCATTGT
133547 CGAT
66 CGAT
* ** * *
133551 GATACTCCAACTCTGTTTTTAAACTCATCGAAATTTAAGTCTTATTTTGTCCAAATTATCATTGT
1 GATACTCCAACCCCATTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCATTGT
133616 CG
66 CG
133618 GGTATACTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (69 bp):
GATACTCCAACCCCATTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCATTGT
CGAT
Found at i:135351 original size:16 final size:16
Alignment explanation
Indices: 135330--135363 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
135320 GGAGCCTTCA
135330 CATTTCATCCAAAATG
1 CATTTCATCCAAAATG
135346 CATTTCATCCAAAATG
1 CATTTCATCCAAAATG
135362 CA
1 CA
135364 AGAAAATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.29
Consensus pattern (16 bp):
CATTTCATCCAAAATG
Found at i:135815 original size:113 final size:113
Alignment explanation
Indices: 135613--135840 Score: 413
Period size: 113 Copynumber: 2.0 Consensus size: 113
135603 AGACTAAGTG
135613 ATAGAGATTGCAACCTTTATTTGAAAGAATAACCCAAAAGGTTCAAGGGAAGGCAACAAAACATC
1 ATAGAGATTGCAACCTTTATTTGAAAGAATAACCCAAAAGGTTCAAGGGAAGGCAACAAAACATC
*
135678 TATACTTTATTGGTCATCTTTAGCTTATTCAATATGGTAATATTCAGC
66 TATACTTTATTGGTCATCTGTAGCTTATTCAATATGGTAATATTCAGC
*
135726 ATAGAGATTGCAACCTTTATTTGAAAGAATAACCCAAAGGGTTCAAGGGAAGGCAACAAAACATC
1 ATAGAGATTGCAACCTTTATTTGAAAGAATAACCCAAAAGGTTCAAGGGAAGGCAACAAAACATC
*
135791 TAT-CTTTTATTGGTCATCTGTAGCTTATTCAATTTGGTAATATTCAGC
66 TATAC-TTTATTGGTCATCTGTAGCTTATTCAATATGGTAATATTCAGC
135839 AT
1 AT
135841 CCAGAACTTT
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
112 1 0.01
113 110 0.99
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (113 bp):
ATAGAGATTGCAACCTTTATTTGAAAGAATAACCCAAAAGGTTCAAGGGAAGGCAACAAAACATC
TATACTTTATTGGTCATCTGTAGCTTATTCAATATGGTAATATTCAGC
Found at i:137284 original size:13 final size:13
Alignment explanation
Indices: 137242--137301 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
137232 GATTTAAAAA
* *
137242 TTTATATAATCAT
1 TTTATATTATAAT
*
137255 ATTATATTCATATAT
1 TTTATATT-ATA-AT
137270 TTTATATTATAAT
1 TTTATATTATAAT
*
137283 TTTAT-TTAAAAT
1 TTTATATTATAAT
*
137295 ATTATAT
1 TTTATAT
137302 ATTTTATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.26
13 14 0.37
14 5 0.13
15 9 0.24
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTATATTATAAT
Found at i:137331 original size:32 final size:34
Alignment explanation
Indices: 137255--137344 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 34
137245 ATATAATCAT
* *
137255 ATTATATTCATATATTTTATATTATAATTTTATTTAA
1 ATTA-ATT-ATATATTTTATA-TAAAATTTTATATAA
*
137292 AAT-ATTATATATTTTATA-AAAATTTTA-ATAA
1 ATTAATTATATATTTTATATAAAATTTTATATAA
* *
137323 ATTAATTATTTATATTATATAA
1 ATTAATTATATATTTTATATAA
137345 TTTTGTATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
31 5 0.11
32 21 0.47
33 2 0.04
34 12 0.27
35 3 0.07
37 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (34 bp):
ATTAATTATATATTTTATATAAAATTTTATATAA
Found at i:137347 original size:14 final size:15
Alignment explanation
Indices: 137329--137424 Score: 60
Period size: 14 Copynumber: 6.4 Consensus size: 15
137319 ATAAATTAAT
137329 TATTTATATTATATA
1 TATTTATATTATATA
*
137344 -ATTT-T-GTATATA
1 TATTTATATTATATA
137356 TATTTATAAATTCATATTA
1 TATTTAT--ATT-ATA-TA
137375 TATTTATATTAT-TA
1 TATTTATATTATATA
* *
137389 -ATATTATATTTTAATT
1 TAT-TTATATTAT-ATA
*
137405 TTTTTATATTATAT-
1 TATTTATATTATATA
137419 TATTTA
1 TATTTA
137425 ACTACAATGT
Statistics
Matches: 63, Mismatches: 7, Indels: 23
0.68 0.08 0.25
Matches are distributed among these distances:
12 6 0.10
13 7 0.11
14 20 0.32
15 2 0.03
16 11 0.17
17 5 0.08
18 3 0.05
19 9 0.14
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (15 bp):
TATTTATATTATATA
Found at i:137393 original size:6 final size:5
Alignment explanation
Indices: 137253--137421 Score: 59
Period size: 5 Copynumber: 34.4 Consensus size: 5
137243 TTATATAATC
* * **
137253 ATATT ATATT CATA-T ATTTT ATATT ATAATT TTATT -TAAA ATATT ATA-T
1 ATATT ATATT -ATATT ATATT ATATT AT-ATT ATATT ATATT ATATT ATATT
* * * * * * * *
137302 ATTTT ATA-A AAATT TTAAT AAATT A-ATT AT-TT ATATT ATATA ATTTT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
* * *
137349 GTATAT ATATT -TA-T AAATT CATATT ATATTT ATATT AT-TA ATATT
1 ATAT-T ATATT ATATT ATATT -ATATT ATA-TT ATATT ATATT ATATT
* * *
137394 ATATT TTAATT TTTTT ATATT ATATT AT
1 ATATT AT-ATT ATATT ATATT ATATT AT
137422 TTAACTACAA
Statistics
Matches: 117, Mismatches: 32, Indels: 30
0.65 0.18 0.17
Matches are distributed among these distances:
3 1 0.01
4 23 0.20
5 68 0.58
6 25 0.21
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:137394 original size:20 final size:19
Alignment explanation
Indices: 137319--137399 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 19
137309 AAAAATTTTA
137319 ATAAATTAATTATTTATATTAT
1 ATAAATTAA-TA-TTATATT-T
* **
137341 ATAATTTTGTATATATATTT
1 ATAAATTAATAT-TATATTT
*
137361 ATAAATTCATATTATATTT
1 ATAAATTAATATTATATTT
*
137380 ATATTATTAATATTATATTT
1 ATA-AATTAATATTATATTT
137400 TAATTTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
19 10 0.20
20 25 0.51
21 8 0.16
22 6 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
ATAAATTAATATTATATTT
Found at i:137853 original size:22 final size:22
Alignment explanation
Indices: 137804--137853 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
137794 AATTATTGAC
*
137804 TAAAATTTAATTAATTTAAATA
1 TAAAATTTAATTAATTCAAATA
* *
137826 TTAAATTTAATTGATTCAAA-A
1 TAAAATTTAATTAATTCAAATA
137847 TCAAAAT
1 T-AAAAT
137854 GATATGAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAATTTAATTAATTCAAATA
Found at i:137901 original size:16 final size:16
Alignment explanation
Indices: 137882--137917 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
137872 TGTGAAACTG
*
137882 AAATAATTTAAACTTA
1 AAATAACTTAAACTTA
*
137898 AAATAACTTAAATTTA
1 AAATAACTTAAACTTA
137914 AAAT
1 AAAT
137918 TATAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAACTTAAACTTA
Found at i:138266 original size:9 final size:10
Alignment explanation
Indices: 138248--138295 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
138238 ATATTATTAT
138248 AAAATATAAA
1 AAAATATAAA
138258 AAAAT-TAAA
1 AAAATATAAA
138267 ATATAATATAAA
1 A-A-AATATAAA
138279 TAAAATATAAA
1 -AAAATATAAA
*
138290 TAAATA
1 AAAATA
138296 AATATTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 5 0.15
10 11 0.33
11 11 0.33
12 5 0.15
13 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATATAAA
Found at i:138266 original size:16 final size:16
Alignment explanation
Indices: 138247--138333 Score: 74
Period size: 16 Copynumber: 5.5 Consensus size: 16
138237 TATATTATTA
*
138247 TAAAATATAAAAAAAT
1 TAAAATATAAATAAAT
138263 TAAAATATAATATAAA-
1 TAAAATATAA-ATAAAT
138279 TAAAATATAAATAAA-
1 TAAAATATAAATAAAT
* * *
138294 TAAATATTTTAA-AATT
1 TAAA-ATATAAATAAAT
*
138310 TAATAATATAAAT-TAT
1 TAA-AATATAAATAAAT
138326 TAAAATAT
1 TAAAATAT
138334 TAAAATTTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
15 16 0.28
16 37 0.64
17 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATATAAATAAAT
Found at i:138285 original size:11 final size:11
Alignment explanation
Indices: 138246--138293 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
138236 TTATATTATT
138246 ATAAAATATAA
1 ATAAAATATAA
138257 A-AAAAT-TAAA
1 ATAAAATAT-AA
*
138267 ATATAATATAA
1 ATAAAATATAA
138278 ATAAAATATAA
1 ATAAAATATAA
138289 ATAAA
1 ATAAA
138294 TAAATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 1 0.03
10 8 0.25
11 22 0.69
12 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAAATATAA
Found at i:138306 original size:24 final size:24
Alignment explanation
Indices: 138279--138333 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
138269 ATAATATAAA
*
138279 TAAAATATAAATAA-ATAAATATTT
1 TAAAATATAAATAATATAAAT-TAT
*
138303 TAAAAT-TTAATAATATAAATTAT
1 TAAAATATAAATAATATAAATTAT
138326 TAAAATAT
1 TAAAATAT
138334 TAAAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAAATATAAATAATATAAATTAT
Found at i:138318 original size:32 final size:29
Alignment explanation
Indices: 138282--138377 Score: 101
Period size: 31 Copynumber: 3.3 Consensus size: 29
138272 ATATAAATAA
138282 AATATAAATAAATAAATATTTTAAAATTT
1 AATATAAATAAATAAATATTTTAAAATTT
* * *
138311 AATA-ATATAAATTATTAAAATATTAAAATTT
1 AATATAAATAAA-TA--AATATTTTAAAATTT
*
138342 -ATATAAATAAA-AAATATTTT-AAATAT
1 AATATAAATAAATAAATATTTTAAAATTT
138368 AATATAAATA
1 AATATAAATA
138378 TATTAAAATC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
26 5 0.09
27 15 0.27
28 6 0.11
29 7 0.13
30 3 0.05
31 19 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AATATAAATAAATAAATATTTTAAAATTT
Found at i:138337 original size:16 final size:16
Alignment explanation
Indices: 138227--138337 Score: 52
Period size: 16 Copynumber: 6.9 Consensus size: 16
138217 GATCTCACAA
*
138227 TATTAAAA-ATTATAT
1 TATTAAAATATTAAAT
* *
138242 TATTATAAAATATAAAAA
1 TA-T-TAAAATATTAAAT
*
138260 AATTAAAATA-TAATAT
1 TATTAAAATATTAA-AT
* *
138276 AAATAAAATA-TAAAT
1 TATTAAAATATTAAAT
* * * *
138291 AAATAAATATTTTAAAA
1 TATTAAA-ATATTAAAT
138308 T-TTAATAATA-TAAAT
1 TATTAA-AATATTAAAT
138323 TATTAAAATATTAAA
1 TATTAAAATATTAAA
138338 ATTTATATAA
Statistics
Matches: 74, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
15 22 0.30
16 36 0.49
17 11 0.15
18 5 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATTAAAATATTAAAT
Found at i:138393 original size:55 final size:58
Alignment explanation
Indices: 138283--138393 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 58
138273 TATAAATAAA
*
138283 ATATAAATAAATAAATATTTTAAAATTTAATAATATAAATTATTAAAATATTAAAATTT
1 ATATAAATAAATAAATATTTTAAAA-TTAATAATATAAATTATTAAAATAGTAAAATTT
*
138342 ATATAAATAAA-AAATATTTT-AAA-T-ATAATATAAATATATTAAAATCGTAAAA
1 ATATAAATAAATAAATATTTTAAAATTAATAATATAAAT-TATTAAAATAGTAAAA
138394 AGATAACAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
54 11 0.22
55 15 0.31
57 3 0.06
58 9 0.18
59 11 0.22
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (58 bp):
ATATAAATAAATAAATATTTTAAAATTAATAATATAAATTATTAAAATAGTAAAATTT
Found at i:138663 original size:8 final size:8
Alignment explanation
Indices: 138650--138756 Score: 84
Period size: 8 Copynumber: 13.5 Consensus size: 8
138640 GTATTATATA
138650 ATATAAAT
1 ATATAAAT
138658 ATATAAAT
1 ATATAAAT
138666 ATATTTAAAT
1 ATA--TAAAT
138676 AATATAAA-
1 -ATATAAAT
*
138684 ATATTAAT
1 ATATAAAT
138692 ATATTAAAAT
1 ATA-T-AAAT
*
138702 TTATATAA-
1 ATATA-AAT
138710 ATATAAA-
1 ATATAAAT
138717 ATA-AAAT
1 ATATAAAT
138724 ATAT-AA-
1 ATATAAAT
138730 ATATAAAT
1 ATATAAAT
138738 ATATAAA-
1 ATATAAAT
*
138745 ATATTAAT
1 ATATAAAT
138753 ATAT
1 ATAT
138757 GAAAGATAGC
Statistics
Matches: 82, Mismatches: 5, Indels: 24
0.74 0.05 0.22
Matches are distributed among these distances:
6 7 0.09
7 24 0.29
8 30 0.37
9 8 0.10
10 10 0.12
11 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:138681 original size:32 final size:33
Alignment explanation
Indices: 138645--138734 Score: 103
Period size: 32 Copynumber: 2.7 Consensus size: 33
138635 TGATCGTATT
138645 ATATAATATAAATATATAAATATATTTAAATAA
1 ATATAATATAAATATATAAATATATTTAAATAA
* * * *
138678 TATAAAATATTAATATATTAA-A-ATTTATATAA
1 -ATATAATATAAATATATAAATATATTTAAATAA
*
138710 ATATAAAATAAAATATATAAATATA
1 ATATAATAT-AAATATATAAATATA
138735 AATATATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
31 7 0.16
32 18 0.40
33 2 0.04
34 18 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATTTAAATAA
Found at i:138723 original size:12 final size:14
Alignment explanation
Indices: 138644--138756 Score: 89
Period size: 13 Copynumber: 8.4 Consensus size: 14
138634 ATGATCGTAT
138644 TATAT-AATATAAA
1 TATATAAATATAAA
**
138657 TATATAAATATATT
1 TATATAAATATAAA
*
138671 TAAAT-AATATAAA
1 TATATAAATATAAA
138684 -ATATTAATATATTAAA
1 TATA-TAA-ATA-TAAA
*
138700 -AT-T-TATATAAA
1 TATATAAATATAAA
138711 TATA-AAATA-AAA
1 TATATAAATATAAA
138723 TATATAAATATAAA
1 TATATAAATATAAA
*
138737 TATATAAAATATTAA
1 TATAT-AAATATAAA
138752 TATAT
1 TATAT
138757 GAAAGATAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 20
0.73 0.08 0.18
Matches are distributed among these distances:
11 4 0.05
12 14 0.17
13 20 0.25
14 20 0.25
15 16 0.20
16 6 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATAAATATAAA
Found at i:138728 original size:22 final size:20
Alignment explanation
Indices: 138644--138755 Score: 76
Period size: 21 Copynumber: 5.6 Consensus size: 20
138634 ATGATCGTAT
138644 TATAT-AATATAAATATATAAA
1 TATATAAATATAAA-ATA-AAA
* *
138665 TATATTTAA-ATAATATAAAA
1 TATA-TAAATATAAAATAAAA
*
138685 TAT-TAATATATTAAAAT---T
1 TATATAA-ATA-TAAAATAAAA
138703 TATATAAATATAAAATAAAA
1 TATATAAATATAAAATAAAA
138723 TATATAAATATAAATATATAAA
1 TATATAAATATAAA-ATA-AAA
*
138745 -ATATTAATATA
1 TATATAAATATA
138756 TGAAAGATAG
Statistics
Matches: 74, Mismatches: 6, Indels: 22
0.73 0.06 0.22
Matches are distributed among these distances:
17 6 0.08
18 8 0.11
19 4 0.05
20 21 0.28
21 25 0.34
22 8 0.11
23 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATATAAATATAAAATAAAA
Found at i:138740 original size:32 final size:34
Alignment explanation
Indices: 138644--138743 Score: 116
Period size: 34 Copynumber: 3.0 Consensus size: 34
138634 ATGATCGTAT
* * *
138644 TATATAATATAAATATATAAATATATTTAAATAA
1 TATAAAATATAAATATATAAATATATATATATAA
* *
138678 TATAAAATATTAATATATTAAA-ATTTATATA-AA
1 TATAAAATATAAATATA-TAAATATATATATATAA
*
138711 TATAAAATA-AAATATATAAATATAAATATATAA
1 TATAAAATATAAATATATAAATATATATATATAA
138744 AATATTAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
31 4 0.07
32 13 0.24
33 13 0.24
34 21 0.38
35 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
TATAAAATATAAATATATAAATATATATATATAA
Found at i:142174 original size:29 final size:28
Alignment explanation
Indices: 142122--142205 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
142112 TTGATAAATT
*
142122 AATAATTTATAT--TA-TATAATTTTTTA
1 AATAATTTATATCATATTTTAA-TTTTTA
142148 AATCAATTTATAT-ATTCATTTT-ATTTTTA
1 AAT-AATTTATATCA-T-ATTTTAATTTTTA
*
142177 AATTATTTATATCATATTTTAATTTTTA
1 AATAATTTATATCATATTTTAATTTTTA
142205 A
1 A
142206 TATTATATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
26 3 0.06
27 14 0.29
28 17 0.35
29 11 0.22
30 2 0.04
31 2 0.04
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
AATAATTTATATCATATTTTAATTTTTA
Found at i:142185 original size:28 final size:28
Alignment explanation
Indices: 142142--142216 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
142132 ATTATATAAT
*
142142 TTTTTAAATCAATTTATAT-ATTCATTTT-A
1 TTTTTAAAT-TATTTATATCA-T-ATTTTAA
142171 TTTTTAAATTATTTATATCATATTTTAA
1 TTTTTAAATTATTTATATCATATTTTAA
142199 TTTTTAATATTATATTAT
1 TTTTTAA-ATTAT-TTAT
142217 TTAACTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 5 0.12
28 17 0.41
29 15 0.37
30 4 0.10
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTAAATTATTTATATCATATTTTAA
Found at i:142200 original size:20 final size:21
Alignment explanation
Indices: 142172--142214 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
142162 TTCATTTTAT
142172 TTTTAAATTATTT-ATATCATA
1 TTTTAAATT-TTTAATATCATA
*
142193 TTTT-AATTTTTAATATTATA
1 TTTTAAATTTTTAATATCATA
142213 TT
1 TT
142215 ATTTAACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 13 0.65
21 4 0.20
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAAATTTTTAATATCATA
Found at i:143144 original size:23 final size:23
Alignment explanation
Indices: 143118--143162 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
143108 CGAATTAAAA
*
143118 TATAAAATA-AATATTTTAAAATG
1 TATAAAATATAA-ATTATAAAATG
*
143141 TATATAATATAAATTATAAAAT
1 TATAAAATATAAATTATAAAAT
143163 AATAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TATAAAATATAAATTATAAAATG
Found at i:143167 original size:15 final size:15
Alignment explanation
Indices: 143136--143185 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
143126 AAATATTTTA
*
143136 AAATGTATATAAT-AT
1 AAAT-TATAAAATAAT
143151 AAATTATAAAATAAT
1 AAATTATAAAATAAT
143166 AAATT-TATAAATAGAT
1 AAATTATA-AAATA-AT
143182 AAAT
1 AAAT
143186 ATTTTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 9 0.29
15 16 0.52
16 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (15 bp):
AAATTATAAAATAAT
Found at i:143258 original size:31 final size:28
Alignment explanation
Indices: 143192--143259 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 28
143182 AAATATTTTT
143192 AATATAATATAATATATAAAAAAATATA
1 AATATAATATAATATATAAAAAAATATA
* *
143220 AATATAATATAAATATATAATGAAATTATA
1 AATATAATAT-AATATATAA-AAAAATATA
143250 AATGATAATA
1 AAT-ATAATA
143260 GCATACTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 10 0.29
29 9 0.26
30 10 0.29
31 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
AATATAATATAATATATAAAAAAATATA
Found at i:143514 original size:23 final size:21
Alignment explanation
Indices: 143488--143543 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
143478 AATGACGTAT
143488 TATTATTAAAAAAAATAATATAA
1 TATTATTAAAAAAAAT-AT-TAA
*
143511 TATTATCTAACATAAAATATTAA
1 TATTAT-TAA-AAAAAATATTAA
143534 TA-TATTAAAA
1 TATTATTAAAA
143544 TTTATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 1 0.03
21 3 0.10
22 3 0.10
23 11 0.38
24 5 0.17
25 6 0.21
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTATTAAAAAAAATATTAA
Found at i:143555 original size:20 final size:21
Alignment explanation
Indices: 143527--143583 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
143517 CTAACATAAA
* *
143527 ATATTAATATATTA-AAATTT
1 ATATAAATATATAATAAATTT
143547 ATATAAATATATAATAAATTT
1 ATATAAATATATAATAAATTT
143568 ACTATAAATA-ATAATA
1 A-TATAAATATATAATA
143584 TAATATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 12 0.36
21 13 0.39
22 8 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAAATATATAATAAATTT
Found at i:143564 original size:22 final size:23
Alignment explanation
Indices: 143533--143583 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
143523 TAAAATATTA
*
143533 ATATATTAAAATTTA-TATAAAT
1 ATATAATAAAATTTACTATAAAT
143555 ATATAAT-AAATTTACTATAAAT
1 ATATAATAAAATTTACTATAAAT
143577 A-ATAATA
1 ATATAATA
143584 TAATATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAATAAAATTTACTATAAAT
Found at i:143595 original size:22 final size:22
Alignment explanation
Indices: 143526--143595 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
143516 TCTAACATAA
* *
143526 AATATTAATATATTA-AAAT-T
1 AATATAAATATATAATAAATAT
* *
143546 TATATAAATATATAATAAATTT
1 AATATAAATATATAATAAATAT
*
143568 ACTATAAATA-ATAATATAATAT
1 AATATAAATATATAATA-AATAT
143590 AATATA
1 AATATA
143596 TAAATTTGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 12 0.30
21 10 0.25
22 18 0.45
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATAAATATATAATAAATAT
Found at i:144325 original size:30 final size:26
Alignment explanation
Indices: 144290--144358 Score: 66
Period size: 30 Copynumber: 2.4 Consensus size: 26
144280 TTAAAATTGT
144290 TAAAATTAAACTCAAAATATAAAATATATA
1 TAAAATTAAA-T-AAAATATAAAA-A-ATA
*
144320 TAAAATATGATATAAAATATAAAAAATA
1 TAAAAT-T-AAATAAAATATAAAAAATA
144348 TAAATATTAAA
1 TAAA-ATTAAA
144359 AATATTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 2 0.06
28 8 0.24
29 3 0.09
30 17 0.50
31 2 0.06
32 2 0.06
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (26 bp):
TAAAATTAAATAAAATATAAAAAATA
Found at i:144332 original size:23 final size:22
Alignment explanation
Indices: 144306--144403 Score: 84
Period size: 23 Copynumber: 4.5 Consensus size: 22
144296 TAAACTCAAA
144306 ATATAAAATATATATAAAATAT
1 ATATAAAATATATATAAAATAT
144328 GATATAAAATATA-A-AAAATAT
1 -ATATAAAATATATATAAAATAT
144349 AAATATTAAAA-ATAT-T--AATAT
1 --ATA-TAAAATATATATAAAATAT
*
144370 ATAAAAAATTATAATATAAAATA-
1 ATATAAAA-TAT-ATATAAAATAT
144393 ATATAAAATAT
1 ATATAAAATAT
144404 TAATATATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
18 4 0.06
19 3 0.05
20 2 0.03
21 14 0.23
22 11 0.18
23 24 0.39
24 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (22 bp):
ATATAAAATATATATAAAATAT
Found at i:144334 original size:12 final size:11
Alignment explanation
Indices: 144306--144403 Score: 84
Period size: 11 Copynumber: 9.0 Consensus size: 11
144296 TAAACTCAAA
144306 ATATAAAATAT
1 ATATAAAATAT
144317 ATATAAAATAT
1 ATATAAAATAT
144328 GATATAAAATAT
1 -ATATAAAATAT
144340 A-A-AAAATAT
1 ATATAAAATAT
144349 AAATATTAAAA-AT
1 --ATA-TAAAATAT
144362 AT-T--AATAT
1 ATATAAAATAT
*
144370 ATAAAAAATTAT
1 ATATAAAA-TAT
144382 AATATAAAATA-
1 -ATATAAAATAT
144393 ATATAAAATAT
1 ATATAAAATAT
144404 TAATATATAA
Statistics
Matches: 72, Mismatches: 2, Indels: 26
0.72 0.02 0.26
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 8 0.11
10 11 0.15
11 17 0.24
12 17 0.24
13 9 0.12
14 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (11 bp):
ATATAAAATAT
Found at i:144354 original size:15 final size:15
Alignment explanation
Indices: 144329--144399 Score: 81
Period size: 15 Copynumber: 4.5 Consensus size: 15
144319 ATAAAATATG
144329 ATATAAAATATAAAAA
1 ATAT-AAATATAAAAA
*
144345 ATATAAATATTAAAA
1 ATATAAATATAAAAA
144360 ATATTAATATATAAAAA
1 ATA-TAA-ATATAAAAA
144377 AT-TATAATATAAAATA
1 ATATA-AATATAAAA-A
144393 ATATAAA
1 ATATAAA
144400 ATATTAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
15 23 0.48
16 13 0.27
17 12 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATATAAATATAAAAA
Found at i:144407 original size:23 final size:23
Alignment explanation
Indices: 144305--144429 Score: 79
Period size: 23 Copynumber: 5.5 Consensus size: 23
144295 TTAAACTCAA
144305 AATATAAAATA-T-ATATAAAAT
1 AATATAAAATATTAATATAAAAT
* *
144326 ATGATATAAAATATAAAAAATATAAAT
1 A--ATATAAAATAT-TAATATA-AAAT
*
144353 ATTA-AAAATATTAATAT---AT
1 AATATAAAATATTAATATAAAAT
*
144372 AA-A-AAATTA-TAATATAAAAT
1 AATATAAAATATTAATATAAAAT
*
144392 AATATAAAATATTAATATATAAAA
1 AATATAAAATATTAATATA-AAAT
144416 AATTATAAATATAT
1 AA-TATAAA-ATAT
144430 AATTTTTTAA
Statistics
Matches: 80, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
17 6 0.08
18 6 0.08
19 3 0.04
20 4 0.05
21 2 0.03
22 5 0.06
23 21 0.26
24 12 0.15
25 8 0.10
26 8 0.10
27 5 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (23 bp):
AATATAAAATATTAATATAAAAT
Found at i:144411 original size:15 final size:15
Alignment explanation
Indices: 144335--144420 Score: 69
Period size: 15 Copynumber: 6.1 Consensus size: 15
144325 TATGATATAA
* *
144335 AATATAAAAAATATA
1 AATATATAAAATATT
144350 AATAT-TAAAAATATT
1 AATATAT-AAAATATT
*
144365 AATATATAAAAAATT
1 AATATATAAAATATT
144380 -ATA-ATATAAA-A-T
1 AATATATA-AAATATT
144392 -A-ATATAAAATATT
1 AATATATAAAATATT
*
144405 AATATATAAAAAATT
1 AATATATAAAATATT
144420 A
1 A
144421 TAAATATATA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
11 4 0.07
12 6 0.10
13 5 0.08
14 7 0.12
15 36 0.61
16 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATATATAAAATATT
Found at i:144411 original size:40 final size:40
Alignment explanation
Indices: 144305--144428 Score: 143
Period size: 40 Copynumber: 3.1 Consensus size: 40
144295 TTAAACTCAA
* *
144305 AATATAAAATATATATAAAATA-TGATATA-AAATATAA--AA
1 AATATAAAATA-ATATAAAATATTAATATATAAA-A-AATTAT
*
144344 AATAT-AAATATTA-AAAATATTAATATATAAAAAATTAT
1 AATATAAAATAATATAAAATATTAATATATAAAAAATTAT
144382 AATATAAAATAATATAAAATATTAATATATAAAAAATTAT
1 AATATAAAATAATATAAAATATTAATATATAAAAAATTAT
144422 AAATATA
1 -AATATA
144429 TAATTTTTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
36 8 0.11
37 9 0.12
38 14 0.19
39 12 0.16
40 25 0.34
41 6 0.08
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (40 bp):
AATATAAAATAATATAAAATATTAATATATAAAAAATTAT
Found at i:148648 original size:2 final size:2
Alignment explanation
Indices: 148641--148687 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
148631 TTTGTTGAAG
*
148641 AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
148683 AT AT A
1 AT AT A
148688 ATTAATATAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:149130 original size:144 final size:143
Alignment explanation
Indices: 148880--149181 Score: 432
Period size: 145 Copynumber: 2.1 Consensus size: 143
148870 GAATTGATCA
* *
148880 ATTAATTAAACTAATTTAATTGAAAATTAAATTTTAATTAATTTAAAATTATATGTAGAATTAAA
1 ATTAATTAAATTAATTTAATTAAAAATTAAATTTTAATTAATTTAAAATTATATGTAGAATTAAA
* * **
148945 ATTTAATTGAATCAATGTAAAATCGATTTGGTTAGTAAAAAA-TATTAAAATTTTAAAAAAACAA
66 ATTTAATTCAATCAACGTAAAATCGATTTAATTAGTAAAAAATTATTAAAATTTTAAAAAAA-AA
149009 AAAAATTATTTTTAC
130 AAAAA-TATTTTTAC
* *
149024 CTTAATTAAATTAATTTAATTAAAAATTAAAATTTTAATTAATTTAAAATTATATGTAGAATTAG
1 ATTAATTAAATTAATTTAATTAAAAATT-AAATTTTAATTAATTTAAAATTATATGTAGAATTAA
* * * *
149089 AATTTAGTTCAATC-ACGTAAAATTGATTTAATTAGTAAAAAATTATTAAAATTTTGAAAAAATA
65 AATTTAATTCAATCAACGTAAAATCGATTTAATTAGTAAAAAATTATTAAAATTTTAAAAAAAAA
*
149153 AAAAATATTTTTAT
130 AAAAATATTTTTAC
149167 ATT--TTAAATTAATTT
1 ATTAATTAAATTAATTT
149182 TTTTTAAAAA
Statistics
Matches: 142, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
141 12 0.08
143 10 0.07
144 55 0.39
145 65 0.46
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (143 bp):
ATTAATTAAATTAATTTAATTAAAAATTAAATTTTAATTAATTTAAAATTATATGTAGAATTAAA
ATTTAATTCAATCAACGTAAAATCGATTTAATTAGTAAAAAATTATTAAAATTTTAAAAAAAAAA
AAAATATTTTTAC
Done.